Re: [Freesurfer] mri_segstats output

Hi Marco, The columns correspond to the integer IDs in the --seg image, so assuming you passed in a binary mask the first column is mean over everything that isn't your ROI and the second column is the mean in your ROI. Cheers, Michael On Wed, Feb 29, 2012 at 10:56 AM, Marco Loggia wrote: > Dea

Re: [Freesurfer] length of a label

sorry, I don't think so On Wed, 29 Feb 2012, Ritobrato Datta wrote: > Hi All, > > Is there a way to calculate the length and width of a label ? > Please let me know. > Thanks a lot > > Ri > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] length of a label

Hi All, Is there a way to calculate the length and width of a label ? Please let me know. Thanks a lot Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi

[Freesurfer] selxavg3 error : NaN in Xtmp.mat file

Hi Doug, I created a new first level analysis along with new contrasts and event numbers for a group of subjects I had previously done analyses on. All but one of the subjects finished selxavg3 without error, but one subject gave the following error: Saving X matrix to /home/sidkundu/freesurfer/

Re: [Freesurfer] Qdec Error: MatrixMultiply: ml is null!

Hi Doug, Below is the output in the terminal window from running the analysis to the crash. Attached are the qdec.fsgd and y.fsgd files from the qdec output. I'm not actually sure what these file represent - could you enlighten me? Thanks! Laura. Number of subjects: 55 Number of factors:4

[Freesurfer] mri_segstats output

Dear all, Given a series of fsaverage-registered rCBF maps, I am trying to extract the average rCBF value from one specific region. This region, which was a significant cluster from a volumetric (fsl) analysis, was binarized and then converted to surface. When I run mri_segstats with the --avgwf

Re: [Freesurfer] tracula - submit via fsl_sub / qsub ?

Hi Andi - Thanks for your kind words! As explained on the trac-all wiki page (and also the help text you get from trac-all --help), the part about not submitting trac-all with pbsubmit is specific to our local Martinos Center users. That's b/c we've modified fsl_sub (and bedpostx) to work on

Re: [Freesurfer] hippocampus volume normalization question

You'll have to run it on each subject. Easy to do with a script. You can then cat the data into one fine (they are just text files). doug Rashmi Singh wrote: > Thanks Doug, > Do I need to run the following for each subject or can is there a way to > run it with input for all my subjects in one

Re: [Freesurfer] problem generate stats data tables

Have you looked at that file to see if there is anything in it? Sometimes the file gets created but not filled with any information (maybe the disk is full). doug Charlotte Bernard wrote: > Dear freesurfer users, > I have tried to run "generate stats data tables", but I have that > error messag

Re: [Freesurfer] strangely low lhCorticalWhiteMatterVol estimate

Hi Mike, can you upload the subject and I'll take a look? doug Michael Harms wrote: > Hello, > > Anyone have a chance to look at this? Should we just forget about > trying to get an accurate lhCorticalWhiteMatterVol value for this > subject? > > thanks, > -MH > > On Tue, 2012-02-21 at 15:35 -060

Re: [Freesurfer] hippocampus volume normalization question

oh, sorry, I do remember now that we took that out (I think we put it back in for the next release). The work-around is to run mri_binarize --i brain.mgz --min 0.1 --count count.dat --o junk.mgh You can delete junk.mgh. The file count.dat will have info about the number of voxels in the bra

Re: [Freesurfer] strangely low lhCorticalWhiteMatterVol estimate

Hello, Anyone have a chance to look at this? Should we just forget about trying to get an accurate lhCorticalWhiteMatterVol value for this subject? thanks, -MH On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote: > Hi guys, > > We have a subject processed with FS v5.1 in which > lhCortical

[Freesurfer] problem generate stats data tables

Dear freesurfer users, I have tried to run "generate stats data tables", but I have that error message: asegstats2table --common-segs --meas volume --tablefile /home/charlotte/TROISCITES/DATA/FREESURFER/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 10049 10053 10079

[Freesurfer] tracula - submit via fsl_sub / qsub ?

Dear Tracula Team, recently i ran trac-all (-prep / -bedp / -path), but I happened to submit the commands to our SGE computer cluster using fsl_sub (which is fsl's wrapper for qsub) According to the header comments of the trac-all script, however, trac-all should not be submitted to a cluster